The unidentified workers were struck just before 5 a.m. on an elevated portion of track near the Yorkdale station on a north-south line, the Toronto Star reported.
The injured man was taken to a trauma center with serious, but non-life-threatening head injuries, CITY-TV said.
TTC Chief Executive Officer Andy Byford rushed to the scene and offered his condolences to the families of the men and said there would be a full investigation into the accident.
The Ontario Ministry of Labor will also investigate, the reports said.
The accident caused mayhem for commuters, as many of the trains that operate throughout the system were parked north of the accident scene and were unable to get into service and there were system-wide subway delays, transit officials said.